Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A1 F1 I3 R2 24 0.0 21072 39.5% 8323 78.9

Breseq alignment

N/A

GATK/CNVnator alignment

BRESEQ :: bam2aln output
GTCAGGAAGAGAAGCAGGTTTCCTTCAACAGCATCTACATGATGGCCGACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCG  >  NZ_CP009273/4177409‑4177508
           |                                                                                        
gcgtaGAAGAGCAGCAGGTCTCCTTCAACAGCATCTACATGATGGCCGACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTGGCAGGTATGCG  >  SRR3722081.6518/6‑100 (MQ=60)
gcgtaGAAGAGCAGCAGGTCTCCTTCAACAGCATCTACATGATGGCCGACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTGGCAGGTATGCG  >  SRR3722081.6645/6‑100 (MQ=60)
           |                                                                                        
GTCAGGAAGAGAAGCAGGTTTCCTTCAACAGCATCTACATGATGGCCGACTCCGGTGCGCGTGGTTCTGCGGCACAGATTCGTCAGCTTGCTGGTATGCG  >  NZ_CP009273/4177409‑4177508

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑